Boeing Co. has agreed to pay $12 million in penalties as part of a sweeping, first-of-its-kind settlement with federal regulators mandating tighter company oversight of suppliers and enhanced quality controls inside its own factories.

The settlement announced Tuesday by the Federal Aviation Administration resolves a total of 13 pending or potential civil-enforcement cases. It also subjects the Chicago-based plane maker to as much as $24 million in additional penalties if it fails to complete all the promised manufacturing,...